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Variant: NM_000277.3(PAH):c.460T>C (p.Tyr154His)

CA229557

102685 (ClinVar)

Gene: PAH
Condition: phenylketonuria
Inheritance Mode: Autosomal recessive inheritance
UUID: 6d4b0dbf-3ec1-4b9d-9a22-949edf5d71fc
Approved on: 2019-12-22
Published on: 2019-12-22

HGVS expressions

NM_000277.3:c.460T>C
NM_000277.3(PAH):c.460T>C (p.Tyr154His)
NC_000012.12:g.102866645A>G
CM000674.2:g.102866645A>G
NC_000012.11:g.103260423A>G
CM000674.1:g.103260423A>G
NC_000012.10:g.101784553A>G
NG_008690.1:g.55958T>C
NG_008690.2:g.96766T>C
NM_000277.1:c.460T>C
NM_000277.2:c.460T>C
NM_001354304.1:c.460T>C
ENST00000307000.7:c.445T>C
ENST00000549111.5:n.556T>C
ENST00000551988.5:n.530+10817T>C
ENST00000553106.5:c.460T>C
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Likely Pathogenic

Met criteria codes 4
PP4_Moderate PM2 PM3 PP3

Evidence Links 4

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Phenylketonuria VCEP
The PAH variant c.460T>C (p.Tyr154His) has been reported in three Chinese individuals with PHA deficiency (Phe levels >120 μM). The PAH variant c.460T>C (p.Tyr154His) was found in trans with the PAH pathogenic variant c.331C>T (p.Arg111Ter)(ClinVar ID: 581) in a Chinese patient with classical PKU (Phe levels >20 mg/dl). All mutations identified were confirmed by analyzing parental DNA. BH4 deficiency was excluded by analysis of urinary pterins and dihydropteridine reductase activity in erythrocytes (PMID: 26322415). The PAH variant c.460T>C (p.Tyr154His) was found as a homozygous occurrence in a Chinese patient with classical PKU (Phe ≥1200 μmol/L) (PM3 Points= 1*0.5=0.5) (PMID:16256386). This variant was also reported in two other Chinese patients with undetermined PKU/MHP phenotype (PMID: 26503515, and PMID: 19915519). The PAH variant c.460T>C (p.Tyr154His) is absent from the gnomAD, ExAC, 1000 Genomes, and ESP population databases. In silico modeling, predictions support that this missense variant could have a deleterious effect on the PAH gene or gene product. This variant is predicted to be deleterious by SIFT, probably damaging by PolyPhen2- HumVar, and disease-causing by Mutation Taster. In summary, this variant meets criteria to be classified as likely pathogenic for PAH. PAH-specific ACMG/AMP criteria applied: PM2, PM3, PP3, and PP4_Moderate.
Met criteria codes
PP4_Moderate
The PAH variant c.460T>C (p.Tyr154His) was found in trans with the PAH pathogenic variant c.331C>T (p.Arg111Ter)(ClinVar ID: 581) in a Chinese patient with classical PKU (Phe levels >20 mg/dl) . All mutations identified in patients were confirmed by analyzing parental DNA. BH4 deficiency was excluded by analysis of urinary pterins and dihydropteridine reductase activity in erythrocytes (PMID: 26322415). This variant was also reported in a Chinese patient with classical PKU (Phe ≥1200 μmol/L) (PMID:16256386), and in two other Chinese patients with undetermined PKU/MHP phenotype (PMID: 26503515, and PMID: 19915519).

PM2
The PAH variant c.460T>C (p.Tyr154His) is absent from the gnomAD, ExAC, 1000 Genomes, and ESP population databases.
PM3
The PAH variant c.460T>C (p.Tyr154His) was found in trans with the PAH pathogenic variant c.331C>T (p.Arg111Ter)(ClinVar ID: 581) in a Chinese patient with classical PKU (Phe levels >20 mg/dl) . All mutations identified in patients were confirmed by analyzing parental DNA. (PM3 Points= 1*1=1) (PMID: 26322415). The PAH variant c.460T>C (p.Tyr154His) was found as a homozygous occurrence in a Chinese patient with classical PKU (Phe ≥1200 μmol/L) (PM3 Points= 1*0.5=0.5) (PMID:16256386) PM3 points awarded in total: 1.5

PP3
In silico modeling, predictions support a deleterious effect on the gene or gene product. This variant is predicted to be deleterious by SIFT, probably damaging by PolyPhen2- HumVar, and disease-causing by Mutation Taster.
Curation History
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